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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGgcatgttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcag

Basic information

species Arabidopsis thaliana
transcript AT3G13870.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G13870.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA07G01230.1 (Glycine max), 5'ss of exon 3
GGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGgcatgttctaatttttgtatacacttcatcagaagaatacttagcttctaattta--tatttatttttccgctgcaattctttgttttcag
| ||||| || || || |||||||||||||| |||||||| ||||| |||||||| ||||  |||||| ||||| |     || |  |||  | |       | ||     |||||||  ||  |   || |   | | || |  |  ||||||||||
GCAAGAGCACACTGTTAAATCATTTGTTTGGTACCAACTTCAGAGAGATGGATGCTTTTAAGGGAAGgtatgttgttgcaattctg-acatgttac------actatcc--cttctaaactaactgggtaatgacctgatgtatatgcttgttttcag

upper sequence: AT3G13870.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 5'ss of exon 3
GGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGgcatgttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttattttt-----ccgctgcaattctttgttttcag
||||||| || || || |||||||||||||| |||||||| || || |||||||| |||||||||||||||||  | ||  |||| |    || ||||      || ||  | | |  ||||     | ||         |     || |  |  ||||||
GGAAGAGCACACTATTAAATCATTTGTTTGGTACCAACTTCAGGGAGATGGATGCTTTTAGAGGAAGgcatgtaatcatgattgtctcgtgttgatcacctttttatttttcattttttttaatcaaacttgggaaagttgacaggatccaattctttcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116444534|gb|EG487126.1|EG487126
EST:     AATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAG                         GTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCC
genomic: AATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGgcatgttcta ... ttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTATTGAGCC
EST: gi|152037947|gb|BP803690.2|BP803690
EST:     AATCATT-GTTTGGAAACAACTTTAGAGAAATGGATGCATTTAGAGGAAG                         GTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGC
genomic: AATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGgcatgttcta ... ttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGC
EST: gi|125123063|gb|EL169512.1|EL169512
EST:     ATCATTTGTTTGGAACCAACTTTAGAGAAATTGGATGCATTTAGAGGAAG                         GTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTA
genomic: ATCATTTGTTTGGAACCAACTTTAGAGAAA-TGGATGCATTTAGAGGAAGgcatgttcta ... ttgttttcagGTCTCAGACGACTAAGGGAATTTGGATTGCTAGATGCGCTGGTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGAGTACGCTCTTGAATCATTTGTTTGGAACCAACTTTAGAGAAATGGATGCATTTAGAGGAAGgcatgttctaatttttgtatacacttcatcagaagaatacttagcttctaatttatatttatttttccgctgcaattctttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA